Hi Fengji
this is a known bug in mris_parcellate. We can give you an updated version if you want, but you should probably rerun all your subjects using it. The good news is that it's fast - just a couple of min/hemi
cheers Bruce On Tue, 26 Jan 2016, Fengji Geng wrote:
Hello fs experts,
We ran a command like ´recon-all -all -s HMN002 -hippocampal-subfields-T1T2 HMN002/T2/*.mgz T1T2´. Then, there was an error as ´Abort (core dumped)´ (which is also attached below). The error log file is also attached here.
Error msg:
setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.775 2015/12/10 21:16:09 fischl Exp $ reading atlas from/cell_root/software/freesurfer/dev/sys/average/lh.curvature.buckner40.fille d.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file.... average std = 1.0 using min determinant for regularization = 0.011 0 singular and 384 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1592 labels changed using aseg relabeling using gibbs priors... 000: 2975 changed, 134786 examined... 001: 698 changed, 12707 examined... 002: 152 changed, 3873 examined... 003: 50 changed, 880 examined... 004: 29 changed, 284 examined... 005: 16 changed, 164 examined... 006: 7 changed, 87 examined... 007: 1 changed, 42 examined... 008: 0 changed, 4 examined... 206 labels changed using aseg 000: 105 total segments, 64 labels (264 vertices) changed 001: 43 total segments, 4 labels (14 vertices) changed 002: 39 total segments, 0 labels (0 vertices) changed 1 filter iterations complete (10 requested, 0 changed) Abort (core dumped) Linux hippocampus.umd.edu 2.6.32-573.12.1.el6.x86_64 #1 SMP Mon Nov 23 12:55:32 EST 2015 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s HMN002 exited with ERRORS at Tue Jan 26 00:23:40 EST 2016
Our freesurfer information: -------- freesurfer-Linux-centos6_x86_64-dev-20151215 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /cell_root/software/freesurfer/dev/sys FSFAST_HOME /cell_root/software/freesurfer/dev/sys/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /export/data/hippocampus/HMN/data MNI_DIR /cell_root/software/freesurfer/dev/sys/mni FSL_DIR /cell_root/software/fsl/new/sys
Looking forward to hearing how we can resolve this error. Also, thanks in advance.
Best,
----- Fengji